On 25/10/2011 5:29 PM, James Starlight wrote:
This was due to that in .gro file corresponded to the end of productive MD I've found this http://i1209.photobucket.com/albums/cc394/own11/mdL.png It's looks like the protein moved out from box so I've thought that some error occured during stimulation
There's no outside to a periodic cell - you will find a matching cavity on the other side of the triclinic periodic cell, where some of the solute atoms actually are also....
GROMACS uses the triclinic representation internally for efficiency - a 2D analogy is that a hexagon tiling a plane can be converted to a rhombus tiling the plane. It doesn't bother wasting your valuable computing cluster time converting back to the initial representation, which probably wasn't wanted. That is, mdrun makes no attempt to guess how you would like your output to appear. See http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions for ideas about how to make your output look as you would like.
Mark
I don't understand this statement. You should also note that a periodic box has no "outside." Perhaps it would be useful to post images online. If you choose to do so, please follow bullet point #4 here: http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette -Justin-- ========================================Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ========================================-- gmx-users mailing list [email protected]<mailto:[email protected]> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected] <mailto:[email protected]>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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